chanjo 3.0.0

Coverage analysis tool for clinical sequencing

<p align="center">
<a href="http://chanjo.co">
<img height="235"
width="244"
src="artwork/logo.png"/>
</a>
</p>

# Chanjo [![PyPI version][fury-image]][fury-url] [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-url]

Chanjo is coverage analysis for clinical sequencing. It's implemented in Python with a command line interface that adheres to [UNIX pipeline philisophy][unix].

## Whats new in Chanjo 3.0? _Radical Red Panda_
Hey - exiting things are coming to the new version of Chanjo :smile:

Chanjo 3 is a significant improvement of the previous versions. You can now extract various metrics directly from Chanjo databases directly from the cli. Try it out!

However, the primary change is [Sambamba][sambamba] integration. Just run `sambamba depth region` and load the output into Chanjo for further data exploration. Chanjo is now more flexible, accurate, and much easier to install. We have also built in some basic commands to quickly extract statistics from the database right from the command line.

## Installation
Chanjo is distruibuted through "pip". Install the latest stable release by running:

```bash
$ pip install chanjo
```

... or locally for development:

```bash
$ git clone https://github.com/robinandeer/chanjo.git && cd chanjo
$ ansible-galaxy install -r provision/requirements.yml
$ vagrant up
$ vagrant ssh
```

## Usage
Chanjo exposes a composable command line interface with a nifty config file implementation.

```bash
$ chanjo init --setup
$ chanjo load /path/to/sambamba.output.bed
$ chanjo calculate mean sample1
{"metrics": {"completeness_10": 90.92, "mean_coverage": 193.85}, "sample_id": "sample1"}
```

## Documentation
Read the Docs is hosting the [official documentation][docs].

I can specifically recommend the fully [interactive demo](http://www.chanjo.co/en/latest/introduction.html#demo), complete with sample data to get you started right away.

If you are looking to learn more about handling sequence coverage data in clinical sequencing, feel free to download and skim through my own [Master's thesis][thesis] and article references.

## Features

### What Chanjo does
Chanjo leverages Sambamba to annotate coverage and completeness for a general BED-file. The output can then easily to loaded into a SQL database that enables investigation of coverage across regions and samples. The database also works as an API to downstream tools like the Chanjo Coverage Report generator.

### What Chanjo doesn't
Chanjo is not the right choice if you care about coverage for every base across the entire genome. Detailed histograms is something [BEDTools][bedtools] already handles with confidence.

## Contributors
- Robin Andeer
- Luca Beltrame ([lbeltrame](https://github.com/lbeltrame))
- John Kern ([kern3020](https://github.com/kern3020))
- Måns Magnusson ([moonso](https://github.com/moonso))

## License
MIT. See the [LICENSE](LICENSE) file for more details.

## Contributing
Anyone can help make this project better - read [CONTRIBUTION](CONTRIBUTION.md) to get started!


[unix]: http://en.wikipedia.org/wiki/Unix_philosophy
[docs]: http://www.chanjo.co/en/latest/
[bedtools]: http://bedtools.readthedocs.org/en/latest/
[thesis]: https://s3.amazonaws.com/tudo/chanjo/RobinAndeerMastersThesisFinal_2013.pdf
[report]: https://github.com/robinandeer/chanjo-report
[sambamba]: http://lomereiter.github.io/sambamba/

[coveralls-url]: https://coveralls.io/r/robinandeer/chanjo
[coveralls-image]: https://img.shields.io/coveralls/robinandeer/chanjo.svg?style=flat

[fury-url]: http://badge.fury.io/py/chanjo
[fury-image]: https://badge.fury.io/py/chanjo.png

[travis-url]: https://travis-ci.org/robinandeer/chanjo
[travis-image]: https://img.shields.io/travis/robinandeer/chanjo.svg?style=flat